annot_df <- annot_df[-which(annot_df$CANARY =='I'),]
ref <- ref[-which(ref$CANARY =='I'),]
#annot_df <- annot_df[-which(annot_df$subtype =='T_cells'),]
dendrogram_barplot <- function(data, dist_method = 'euclidean', 
    hclust_method = 'ward.D', corr_mat = FALSE){
    
    # Dendrogram
    if(corr_mat){
        corr_pt <- Hmisc::rcorr(t(as.matrix(data)), type = 'spearman')
        dist_mat <- dist(corr_pt$r, method = dist_method)
    } else {
        dist_mat <- dist(data, method = dist_method)
    }
    hclust_avg <- hclust(dist_mat, method = hclust_method)
    par(mar=c(2,7,4,2), lwd=2, mgp=c(3,1,0), las=1, font.lab=2)
    plot(hclust_avg,cex = 0.8, hang = -1, main = paste0(hclust_method, ' linkage'))
    
    # Barplot
    coul = brewer.pal(9, "Set1")
    data <- data[hclust_avg$order,] #dendrogram order
    data <- t(as.matrix(data))
    
    par(mgp=c(1.5,0.25,0), las=1, mar = c(3, 5, 1, 7.5), xpd=TRUE, font.lab=2, lwd=1) # axis label locations
    barplot(data,
            col=coul ,
            border='white',
            horiz=TRUE,
            cex.names=0.75,
            cex.axis = 0.75)
    title(xlab="Cell type (% of sample)", mgp = c(1.5, 0.5, 0))
    title(ylab="Patient ID",  mgp = c(3, 0.1, 0))
    legend('topright', legend = rownames(data), fill = coul, ncol = 1, inset=c(-0.3,0),
               cex = 0.75)

}

All cells after denoising

Major cell types

Only major cell types

prcnt_by_pt <- ClassAbundanceByPt(data=annot_df, ptID_col = 'pt_ID', 
    class_col = 'cell_type')
rownames(prcnt_by_pt) <- paste0(rownames(prcnt_by_pt), '_', ref$CANARY)

levels(annot_df$cell_type)
## [1] "Endothelial" "Epithelial"  "Immune"      "Mesenchymal"
# Dendrograms and barplots
dendrogram_barplot(prcnt_by_pt, dist_method = 'euclidean', hclust_method = 'ward.D')

dendrogram_barplot(prcnt_by_pt, dist_method = 'euclidean', hclust_method = 'complete')

# Correlation plot
corr_plot(prcnt_by_pt)

ggpubr::ggscatter(prcnt_by_pt, x = "Endothelial", y = 'Immune',
          add = "reg.line", conf.int = TRUE, combine = TRUE,
          cor.coef = TRUE, cor.method = "spearman", add.params = list(color = 'gray'),
          xlab = "Endothelial cells", ylab = 'Immune cells')
## `geom_smooth()` using formula 'y ~ x'

# Differential abundance
x <- DA_analysis(annot_df, ref, class_col='cell_type', group_levels=c('G','P'),
     group_col = 'CANARY', ptID_col = 'pt_ID')
## 
## Attaching package: 'operators'
## The following objects are masked from 'package:base':
## 
##     options, strrep
## 
## Attaching package: 'dplyr'
## The following object is masked from 'package:operators':
## 
##     %>%
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
x$pvals
##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206

Major cell types and immune subtypes and T cells as a group

## [1] "Endothelial"  "Epithelial"   "Mesenchymal"  "Myeloid"      "NK_cells"    
## [6] "Other_immune" "T_cells"

##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206

Subtypes

All subtypes

##  [1] "Endothelial"   "Epithelial_1"  "Epithelial_10" "Epithelial_2" 
##  [5] "Epithelial_3"  "Epithelial_4"  "Epithelial_5"  "Epithelial_6" 
##  [9] "Epithelial_7"  "Epithelial_8"  "Epithelial_9"  "Mesenchymal"  
## [13] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
## [17] "Tc_cells"      "Th_cells"

##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206
## `geom_smooth()` using formula 'y ~ x'

## `geom_smooth()` using formula 'y ~ x'

Subtypes (T cells as one group)

##  [1] "Endothelial"   "Epithelial_1"  "Epithelial_10" "Epithelial_2" 
##  [5] "Epithelial_3"  "Epithelial_4"  "Epithelial_5"  "Epithelial_6" 
##  [9] "Epithelial_7"  "Epithelial_8"  "Epithelial_9"  "Mesenchymal"  
## [13] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"

##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206

Only Immune

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"

##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"

##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206

Only Epithelial

All Epithelial subtypes

##  [1] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [5] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
##  [9] "Epithelial_8"  "Epithelial_9"

##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206

Stromal cells only

All subtypes

## [1] "Endothelial"  "Mesenchymal"  "Myeloid"      "NK_cells"     "Other_immune"
## [6] "T_cells"      "Tc_cells"     "Th_cells"

##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206

Subtypes (T cells as one group)

## [1] "Endothelial"  "Mesenchymal"  "Myeloid"      "NK_cells"     "Other_immune"
## [6] "T_cells"

##     cell_type   p.value FDR_corrected
## 1 Endothelial 0.1714286     0.6349206
## 2  Epithelial 0.9142857     0.9142857
## 3      Immune 0.3523810     0.6349206
## 4 Mesenchymal 0.4761905     0.6349206

Differential protein expression

med_endo <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='cell_type',
    celltype_name='Endothelial', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))

med_epi <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='cell_type',
    celltype_name='Epithelial', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_fibmes <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='cell_type',
    celltype_name='Mesenchymal', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_imm <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='cell_type',
    celltype_name='Immune', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_tcells <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype2',
    celltype_name='T_cells', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_CD8T <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype',
    celltype_name='Tc_cells', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))

med_CD4T <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype',
    celltype_name='Th_cells', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_mye <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype',
    celltype_name='Myeloid', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_NK <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype',
    celltype_name='NK_cells', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51), 
    ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties

Endothelial cells

## Using CANARY, pt_ID as id variables

##              Protein   p.value FDR_corrected
## 1      144Nd_HLA-ABC 0.1714286     0.7619048
## 2         145Nd_CD31 0.4761905     0.7619048
## 3  146Nd_Thioredoxin 0.3523810     0.7619048
## 4        147Sm_b-CAT 0.4761905     0.7619048
## 5     156Gd_Vimentin 1.0000000     1.0000000
## 6      158Gd_p-STAT3 0.7619048     0.8465608
## 7         160Gd_MDM2 0.6095238     0.7619048
## 8  161Dy_Cytokeratin 0.4761905     0.7619048
## 9         163Dy_TP63 0.6095238     0.7619048
## 10      174Yb_HLA-DR 0.1714286     0.7619048
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Fibroblasts/Mesenchymal cells

## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(0, 0.0958118253303701, 0.284162729407862, :
## cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.802649816095183, 0.215492384630114,
## 0.0605647943338007, : cannot compute exact p-value with ties

##          Protein    p.value FDR_corrected
## 1    141Pr_EpCAM 0.76190476     0.9142857
## 2   142Nd_ccasp3 0.91428571     0.9142857
## 3     155Gd_CD56 0.47619048     0.8571429
## 4 156Gd_Vimentin 0.91428571     0.9142857
## 5  158Gd_p-STAT3 0.11428571     0.5142857
## 6     160Gd_MDM2 0.19945761     0.5983728
## 7     163Dy_TP63 0.47619048     0.8571429
## 8      170Yb_CD3 0.91406196     0.9142857
## 9   174Yb_HLA-DR 0.03809524     0.3428571
## Warning in wilcox.test.default(c(0, 0.0958118253303701, 0.284162729407862, :
## cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.802649816095183, 0.215492384630114,
## 0.0605647943338007, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Immune cells

## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(3.06708656196431, 0.066910551904235,
## 3.04431780411568, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.202586121632867, 0.0645635010399363, : cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(c(0.501727573634015, 0.130067040154415,
## 0.712432219756351, : cannot compute exact p-value with ties

##           Protein   p.value FDR_corrected
## 1   144Nd_HLA-ABC 0.1055017     0.8571429
## 2      154Sm_CD45 0.4761905     0.9523810
## 3  156Gd_Vimentin 0.4761905     0.9523810
## 4   158Gd_p-STAT3 0.7619048     0.9523810
## 5       159Tb_CD4 0.9140620     1.0000000
## 6      163Dy_TP63 0.6095238     0.9523810
## 7      166Er_CD44 1.0000000     1.0000000
## 8       170Yb_CD3 0.7619048     0.9523810
## 9     171Yb_CD11b 0.3314247     0.9523810
## 10   174Yb_HLA-DR 0.1714286     0.8571429
## Warning: Removed 1 rows containing non-finite values (stat_boxplot).
## Warning: Removed 1 rows containing non-finite values (stat_signif).
## Warning in wilcox.test.default(c(3.06708656196431, 0.066910551904235,
## 3.04431780411568, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.202586121632867, 0.0645635010399363, : cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(c(0.501727573634015, 0.130067040154415,
## 0.712432219756351, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

T cells

## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(3.08923421925895, 0.0448292529698694,
## 2.91669547906524, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.15951925690942, 0.142600017626425,
## 1.11836487985089, : cannot compute exact p-value with ties

##          Protein    p.value FDR_corrected
## 1  144Nd_HLA-ABC 0.06656797     0.5325437
## 2     154Sm_CD45 0.25714286     0.6349206
## 3 156Gd_Vimentin 0.47619048     0.6349206
## 4      159Tb_CD4 0.74838121     0.8552928
## 5     163Dy_TP63 0.91428571     0.9142857
## 6     166Er_CD44 0.25714286     0.6349206
## 7      170Yb_CD3 0.35238095     0.6349206
## 8   174Yb_HLA-DR 0.47619048     0.6349206
## Warning in wilcox.test.default(c(3.08923421925895, 0.0448292529698694,
## 2.91669547906524, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.15951925690942, 0.142600017626425,
## 1.11836487985089, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

CD8 T cells

## Using CANARY, pt_ID as id variables

##          Protein    p.value FDR_corrected
## 1  144Nd_HLA-ABC 0.03174603     0.2539683
## 2     154Sm_CD45 0.90476190     0.9047619
## 3 156Gd_Vimentin 0.55555556     0.8344671
## 4     163Dy_TP63 0.19047619     0.5079365
## 5     166Er_CD44 0.73015873     0.8344671
## 6      168Er_CD8 0.55555556     0.8344671
## 7      170Yb_CD3 0.73015873     0.8344671
## 8   174Yb_HLA-DR 0.11111111     0.4444444
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

CD4 T cells

## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(0, 0.0561621657336121, 0, 0), c(0, 0,
## 1.50456532271426, : cannot compute exact p-value with ties

##          Protein   p.value FDR_corrected
## 1  144Nd_HLA-ABC 0.6095238     0.9142857
## 2     154Sm_CD45 0.3523810     0.7928571
## 3 156Gd_Vimentin 0.2571429     0.7714286
## 4      159Tb_CD4 0.6095238     0.9142857
## 5     163Dy_TP63 0.7619048     0.9795918
## 6     166Er_CD44 0.1714286     0.7714286
## 7     169Tm_CD24 1.0000000     1.0000000
## 8      170Yb_CD3 0.2571429     0.7714286
## 9   174Yb_HLA-DR 0.9142857     1.0000000
## Warning in wilcox.test.default(c(0, 0.0561621657336121, 0, 0), c(0, 0,
## 1.50456532271426, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Myeloid cells

## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(3.30075534359615, 0.0972935332589382,
## 3.31354462816258, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.62386202915046, 0.717296683223608,
## 2.44717234480325, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.748820669157824, 0.123253874437529,
## 1.67192224879611, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.63662474810693, 0.0913139040611759,
## 1.20841095112529, : cannot compute exact p-value with ties

##              Protein   p.value FDR_corrected
## 1      144Nd_HLA-ABC 0.1645218     0.9523810
## 2         145Nd_CD31 0.4541743     0.9523810
## 3  146Nd_Thioredoxin 0.5929097     0.9846154
## 4         154Sm_CD45 0.4761905     0.9523810
## 5     156Gd_Vimentin 0.4761905     0.9523810
## 6      158Gd_p-STAT3 0.3523810     0.9523810
## 7          159Tb_CD4 0.7461278     0.9846154
## 8         160Gd_MDM2 0.9142857     0.9846154
## 9         163Dy_TP63 1.0000000     1.0000000
## 10        166Er_CD44 0.9142857     0.9846154
## 11       171Yb_CD11b 0.4761905     0.9523810
## 12        172Yb_p-S6 0.9142857     0.9846154
## 13      174Yb_HLA-DR 0.2571429     0.9523810
## 14       175Lu_PD-L1 0.7619048     0.9846154
## Warning: Removed 4 rows containing non-finite values (stat_boxplot).
## Warning: Removed 4 rows containing non-finite values (stat_signif).
## Warning in wilcox.test.default(c(3.30075534359615, 0.0972935332589382,
## 3.31354462816258, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.62386202915046, 0.717296683223608,
## 2.44717234480325, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.748820669157824, 0.123253874437529,
## 1.67192224879611, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.63662474810693, 0.0913139040611759,
## 1.20841095112529, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

NK cells

## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(1.64257353775631, 0.200933284463877,
## 1.65031204702996, : cannot compute exact p-value with ties

##              Protein    p.value FDR_corrected
## 1       142Nd_ccasp3 0.60952381     0.7757576
## 2      144Nd_HLA-ABC 0.11428571     0.3428571
## 3         145Nd_CD31 0.17142857     0.3428571
## 4  146Nd_Thioredoxin 0.16452182     0.3428571
## 5         148Nd_HER2 0.17142857     0.3428571
## 6         154Sm_CD45 0.47619048     0.6666667
## 7         155Gd_CD56 1.00000000     1.0000000
## 8     156Gd_Vimentin 0.17142857     0.3428571
## 9      158Gd_p-STAT3 0.91428571     0.9846154
## 10        160Gd_MDM2 0.47619048     0.6666667
## 11        163Dy_TP63 0.03809524     0.2666667
## 12        166Er_CD44 0.76190476     0.8888889
## 13        172Yb_p-S6 0.25714286     0.4500000
## 14      174Yb_HLA-DR 0.03809524     0.2666667
## Warning: Removed 4 rows containing non-finite values (stat_boxplot).
## Warning: Removed 4 rows containing non-finite values (stat_signif).
## Warning in wilcox.test.default(c(1.64257353775631, 0.200933284463877,
## 1.65031204702996, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Epithelial cells

## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(2.33079293987923, 0.0582644008491126,
## 1.75087785796523, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.63156525887895, 0.322305842850225,
## 1.32203451663395, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.13653172069154, 0.0527562183492093,
## 1.50292979733778, : cannot compute exact p-value with ties

##              Protein    p.value FDR_corrected
## 1        141Pr_EpCAM 0.11428571     0.4114286
## 2       142Nd_ccasp3 0.35238095     0.5714286
## 3      144Nd_HLA-ABC 0.16452182     0.4408163
## 4        147Sm_b-CAT 0.17142857     0.4408163
## 5         148Nd_HER2 0.03809524     0.4114286
## 6         151Eu_TTF1 0.09898793     0.4114286
## 7         154Sm_CD45 0.47619048     0.5714286
## 8         155Gd_CD56 0.76190476     0.8067227
## 9     156Gd_Vimentin 0.47619048     0.5714286
## 10     158Gd_p-STAT3 0.35238095     0.5714286
## 11        160Gd_MDM2 0.91428571     0.9142857
## 12 161Dy_Cytokeratin 0.11428571     0.4114286
## 13         162Dy_MET 0.25714286     0.5142857
## 14        163Dy_TP63 0.47619048     0.5714286
## 15         164Dy_CK7 0.47619048     0.5714286
## 16        165Ho_EGFR 0.10550173     0.4114286
## 17         170Yb_CD3 0.60952381     0.6857143
## 18      174Yb_HLA-DR 0.25714286     0.5142857
## Warning in wilcox.test.default(c(2.33079293987923, 0.0582644008491126,
## 1.75087785796523, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.63156525887895, 0.322305842850225,
## 1.32203451663395, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.13653172069154, 0.0527562183492093,
## 1.50292979733778, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Cell type viz

# sampling 1k cells per sample

# tSNE
# UMAP